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| Status |
Public on Dec 01, 2019 |
| Title |
Epigenetic profiling of mouse bone marrow derived mast cells (BMMCs) [ChIP-seq] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Allergy is one of the least understood immunological response partly due to the diversity of allergens and the complexity of immune response against them. In allergic responses, mast cells are key players with their ability to rapidly degranulate and also generate de novo lipids and transcripts. Although the molecular details of degranulation in mast cell were studied in allergic inflammation, the transcriptional response involving chromatin remodeling, enhancer dynamics and long non-coding RNA (lncRNA) expression are largely unexplored. Here, using mouse bone marrow derived mast cells (BMMCs), we characterized the steady state, immunoglobulin E (IgE) and antigen (Ag) mediated epigenetic changes in mast cell chromatin and described the enhancer, super-enhancer and mRNA, lncRNA catalogue in these cells.
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| Overall design |
BMMCs were generated from mouse bone marrow cells with IL-3 and SCF. Cells were left untreated or sensitized overnight with DNP-IgE (0.5 ug/ml) and treated with DNP-BSA (50 ng/ml) for 2h. H3K4me1, H3K4me3 and H3K27Ac CHIP-seq was performed.
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| Contributor(s) |
Cildir G, Zhang J |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Nov 30, 2015 |
| Last update date |
Dec 01, 2019 |
| Contact name |
Jingxian Zhang |
| E-mail(s) |
zhangjingxian.nus@gmail.com
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| Organization name |
Institute of Molecular and Cell Biology (IMCB), A-Star, Singapore
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| Department |
IMCB
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| Street address |
61 Biopolis Drive Proteos
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| City |
Singapore |
| State/province |
Singpaore |
| ZIP/Postal code |
138673 |
| Country |
Singapore |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (20)
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| GSM1958529 |
ChIP-Seq input for H3K4me1, H3K4me3, H3K27Ac rep 1 |
| GSM1958530 |
ChIP-Seq input for H3K4me1, H3K4me3, H3K27Ac rep 2 |
| GSM1958531 |
ChIP-Seq of H3K27ac in BMMC with DNP-BSA (50 ng/ml) for 2h rep 1 |
| GSM1958532 |
ChIP-Seq of H3K4M1 in BMMC with DNP-BSA (50 ng/ml) for 2h rep 1 |
| GSM1958533 |
ChIP-Seq of H3K4M3 in BMMC with DNP-BSA (50 ng/ml) for 2h rep 1 |
| GSM1958534 |
ChIP-Seq of H3K27ac in BMMC with DNP-BSA (50 ng/ml) for 2h rep 2 |
| GSM1958535 |
ChIP-Seq of H3K4M1 in BMMC with DNP-BSA (50 ng/ml) for 2h rep 2 |
| GSM1958536 |
ChIP-Seq of H3K4M3 in BMMC with DNP-BSA (50 ng/ml) for 2h rep 2 |
| GSM1958537 |
ChIP-Seq of H3K27ac in BMMC sensitized overnight with DNP-IgE (0.5 ug/ml) rep 1 |
| GSM1958538 |
ChIP-Seq of H3K4M1 in BMMC sensitized overnight with DNP-IgE (0.5 ug/ml) rep 1 |
| GSM1958539 |
ChIP-Seq of H3K4M3 in BMMC sensitized overnight with DNP-IgE (0.5 ug/ml) rep 1 |
| GSM1958540 |
ChIP-Seq of H3K27ac in BMMC sensitized overnight with DNP-IgE (0.5 ug/ml) rep 2 |
| GSM1958541 |
ChIP-Seq of H3K4M1 in BMMC sensitized overnight with DNP-IgE (0.5 ug/ml) rep 2 |
| GSM1958542 |
ChIP-Seq of H3K4M3 in BMMC sensitized overnight with DNP-IgE (0.5 ug/ml) rep 2 |
| GSM1958543 |
ChIP-Seq of H3K27ac in untreated BMMC rep 1 |
| GSM1958544 |
ChIP-Seq of H3K4M1 in untreated BMMC rep 1 |
| GSM1958545 |
ChIP-Seq of H3K4M3 in untreated BMMC rep 1 |
| GSM1958546 |
ChIP-Seq of H3K27ac in untreated BMMC rep 2 |
| GSM1958547 |
ChIP-Seq of H3K4M1 in untreated BMMC rep 2 |
| GSM1958548 |
ChIP-Seq of H3K4M3 in untreated BMMC rep 2 |
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| This SubSeries is part of SuperSeries: |
| GSE111547 |
Landscape of mouse mast cell chromatin: a rich resource for identification of novel mediators and genetic drivers of allergic and inflammatory diseases |
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| Relations |
| BioProject |
PRJNA304469 |
| SRA |
SRP066820 |
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